Genome-wide association study identifies new loci for resistance to leptosphaeria maculans in canola

Harsh Raman, Rosy Raman, Neil Coombes, Simon Diffey, Kurt Lindbeck, Denise Barbulescu, Jacqueline Batley, David Edwards, Phil Salisbury, Steve Marcroft

Research output: Contribution to journalArticle

15 Citations (Scopus)

Abstract

Key message “We identified both quantitative and quantitative resistance loci to Leptosphaeria maculans, a fungal pathogen, causing blackleg disease in canola. Several genome-wide significant associations were detected at known and new loci for blackleg resistance. We further validated statistically significant associations in four genetic mapping populations, demonstrating that GWAS marker loci are indeed associated with resistance to L. maculans. One of the novel loci identified for the first time, Rlm12, conveys adult plant resistance in canola.” Blackleg, caused by Leptosphaeria maculans, is a significant disease which affects the sustainable production of canola (Brassica napus). This study reports a genome-wide association study based on 18,804 polymorphic SNPs to identify loci associated with qualitative and quantitative resistance to L. maculans. Genomic regions delimited with 694 significant SNP markers, that are associated with resistance evaluated using 12 single spore isolates and pathotypes from four canola stubble were identified. Several significant associations were detected at known disease resistance loci including in the vicinity of recently cloned Rlm2/LepR3 genes, and at new loci on chromosomes A01/C01, A02/C02, A03/C03, A05/C05, A06, A08, and A09. In addition, we validated statistically significant associations on A01, A07, and A10 in four genetic mapping populations, demonstrating that GWAS marker loci are indeed associated with resistance to L. maculans. One of the novel loci identified for the first time, Rlm12, conveys adult plant resistance and mapped within 13.2 kb from Arabidopsis R gene of TIR-NBS class. We showed that resistance loci are located in the vicinity of R genes of Arabidopsis thaliana and Brassica napus on the sequenced genome of B. napus cv. Darmor-bzh. Significantly associated SNP markers provide a valuable tool to enrich germplasm for favorable alleles in order to improve the level of resistance to L. maculans in canola.
Original languageEnglish
Pages (from-to)1-16
Number of pages16
JournalFrontiers in Plant Science
Volume7
Issue numberOCTOBER2016
DOIs
Publication statusPublished - 2016
Externally publishedYes

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Plenodomus lingam
canola
loci
Brassica napus
mature plants
chromosome mapping
genome-wide association study
genome
genes
stubble
pathotypes
disease resistance
germplasm
Arabidopsis thaliana
spores
Arabidopsis
alleles
chromosomes
genomics

Cite this

Raman, H., Raman, R., Coombes, N., Diffey, S., Lindbeck, K., Barbulescu, D., ... Marcroft, S. (2016). Genome-wide association study identifies new loci for resistance to leptosphaeria maculans in canola. Frontiers in Plant Science, 7(OCTOBER2016), 1-16. https://doi.org/10.3389/fpls.2016.01513
Raman, Harsh ; Raman, Rosy ; Coombes, Neil ; Diffey, Simon ; Lindbeck, Kurt ; Barbulescu, Denise ; Batley, Jacqueline ; Edwards, David ; Salisbury, Phil ; Marcroft, Steve. / Genome-wide association study identifies new loci for resistance to leptosphaeria maculans in canola. In: Frontiers in Plant Science. 2016 ; Vol. 7, No. OCTOBER2016. pp. 1-16.
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abstract = "Key message “We identified both quantitative and quantitative resistance loci to Leptosphaeria maculans, a fungal pathogen, causing blackleg disease in canola. Several genome-wide significant associations were detected at known and new loci for blackleg resistance. We further validated statistically significant associations in four genetic mapping populations, demonstrating that GWAS marker loci are indeed associated with resistance to L. maculans. One of the novel loci identified for the first time, Rlm12, conveys adult plant resistance in canola.” Blackleg, caused by Leptosphaeria maculans, is a significant disease which affects the sustainable production of canola (Brassica napus). This study reports a genome-wide association study based on 18,804 polymorphic SNPs to identify loci associated with qualitative and quantitative resistance to L. maculans. Genomic regions delimited with 694 significant SNP markers, that are associated with resistance evaluated using 12 single spore isolates and pathotypes from four canola stubble were identified. Several significant associations were detected at known disease resistance loci including in the vicinity of recently cloned Rlm2/LepR3 genes, and at new loci on chromosomes A01/C01, A02/C02, A03/C03, A05/C05, A06, A08, and A09. In addition, we validated statistically significant associations on A01, A07, and A10 in four genetic mapping populations, demonstrating that GWAS marker loci are indeed associated with resistance to L. maculans. One of the novel loci identified for the first time, Rlm12, conveys adult plant resistance and mapped within 13.2 kb from Arabidopsis R gene of TIR-NBS class. We showed that resistance loci are located in the vicinity of R genes of Arabidopsis thaliana and Brassica napus on the sequenced genome of B. napus cv. Darmor-bzh. Significantly associated SNP markers provide a valuable tool to enrich germplasm for favorable alleles in order to improve the level of resistance to L. maculans in canola.",
keywords = "Blackleg, Comparative mapping, Genome-wide association analysis, Linkage analysis, Natural variation, Race-specific and race non-specific resistance, Resistance to L. maculans canola",
author = "Harsh Raman and Rosy Raman and Neil Coombes and Simon Diffey and Kurt Lindbeck and Denise Barbulescu and Jacqueline Batley and David Edwards and Phil Salisbury and Steve Marcroft",
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Raman, H, Raman, R, Coombes, N, Diffey, S, Lindbeck, K, Barbulescu, D, Batley, J, Edwards, D, Salisbury, P & Marcroft, S 2016, 'Genome-wide association study identifies new loci for resistance to leptosphaeria maculans in canola', Frontiers in Plant Science, vol. 7, no. OCTOBER2016, pp. 1-16. https://doi.org/10.3389/fpls.2016.01513

Genome-wide association study identifies new loci for resistance to leptosphaeria maculans in canola. / Raman, Harsh; Raman, Rosy; Coombes, Neil; Diffey, Simon; Lindbeck, Kurt; Barbulescu, Denise; Batley, Jacqueline; Edwards, David; Salisbury, Phil; Marcroft, Steve.

In: Frontiers in Plant Science, Vol. 7, No. OCTOBER2016, 2016, p. 1-16.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Genome-wide association study identifies new loci for resistance to leptosphaeria maculans in canola

AU - Raman, Harsh

AU - Raman, Rosy

AU - Coombes, Neil

AU - Diffey, Simon

AU - Lindbeck, Kurt

AU - Barbulescu, Denise

AU - Batley, Jacqueline

AU - Edwards, David

AU - Salisbury, Phil

AU - Marcroft, Steve

PY - 2016

Y1 - 2016

N2 - Key message “We identified both quantitative and quantitative resistance loci to Leptosphaeria maculans, a fungal pathogen, causing blackleg disease in canola. Several genome-wide significant associations were detected at known and new loci for blackleg resistance. We further validated statistically significant associations in four genetic mapping populations, demonstrating that GWAS marker loci are indeed associated with resistance to L. maculans. One of the novel loci identified for the first time, Rlm12, conveys adult plant resistance in canola.” Blackleg, caused by Leptosphaeria maculans, is a significant disease which affects the sustainable production of canola (Brassica napus). This study reports a genome-wide association study based on 18,804 polymorphic SNPs to identify loci associated with qualitative and quantitative resistance to L. maculans. Genomic regions delimited with 694 significant SNP markers, that are associated with resistance evaluated using 12 single spore isolates and pathotypes from four canola stubble were identified. Several significant associations were detected at known disease resistance loci including in the vicinity of recently cloned Rlm2/LepR3 genes, and at new loci on chromosomes A01/C01, A02/C02, A03/C03, A05/C05, A06, A08, and A09. In addition, we validated statistically significant associations on A01, A07, and A10 in four genetic mapping populations, demonstrating that GWAS marker loci are indeed associated with resistance to L. maculans. One of the novel loci identified for the first time, Rlm12, conveys adult plant resistance and mapped within 13.2 kb from Arabidopsis R gene of TIR-NBS class. We showed that resistance loci are located in the vicinity of R genes of Arabidopsis thaliana and Brassica napus on the sequenced genome of B. napus cv. Darmor-bzh. Significantly associated SNP markers provide a valuable tool to enrich germplasm for favorable alleles in order to improve the level of resistance to L. maculans in canola.

AB - Key message “We identified both quantitative and quantitative resistance loci to Leptosphaeria maculans, a fungal pathogen, causing blackleg disease in canola. Several genome-wide significant associations were detected at known and new loci for blackleg resistance. We further validated statistically significant associations in four genetic mapping populations, demonstrating that GWAS marker loci are indeed associated with resistance to L. maculans. One of the novel loci identified for the first time, Rlm12, conveys adult plant resistance in canola.” Blackleg, caused by Leptosphaeria maculans, is a significant disease which affects the sustainable production of canola (Brassica napus). This study reports a genome-wide association study based on 18,804 polymorphic SNPs to identify loci associated with qualitative and quantitative resistance to L. maculans. Genomic regions delimited with 694 significant SNP markers, that are associated with resistance evaluated using 12 single spore isolates and pathotypes from four canola stubble were identified. Several significant associations were detected at known disease resistance loci including in the vicinity of recently cloned Rlm2/LepR3 genes, and at new loci on chromosomes A01/C01, A02/C02, A03/C03, A05/C05, A06, A08, and A09. In addition, we validated statistically significant associations on A01, A07, and A10 in four genetic mapping populations, demonstrating that GWAS marker loci are indeed associated with resistance to L. maculans. One of the novel loci identified for the first time, Rlm12, conveys adult plant resistance and mapped within 13.2 kb from Arabidopsis R gene of TIR-NBS class. We showed that resistance loci are located in the vicinity of R genes of Arabidopsis thaliana and Brassica napus on the sequenced genome of B. napus cv. Darmor-bzh. Significantly associated SNP markers provide a valuable tool to enrich germplasm for favorable alleles in order to improve the level of resistance to L. maculans in canola.

KW - Blackleg

KW - Comparative mapping

KW - Genome-wide association analysis

KW - Linkage analysis

KW - Natural variation

KW - Race-specific and race non-specific resistance

KW - Resistance to L. maculans canola

U2 - 10.3389/fpls.2016.01513

DO - 10.3389/fpls.2016.01513

M3 - Article

VL - 7

SP - 1

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JO - Frontiers in Plant Science

JF - Frontiers in Plant Science

SN - 1664-462X

IS - OCTOBER2016

ER -